Allegan is located at 42°31'45" North, 85°51'19" West (42.529167, -85.855278).

According to the United States Census Bureau, the city has a total area of 4.32 mi2 (11.18 km2). 3.81 mi2 (9.86 km2) of it is land and 0.51 mi2 (1.32 km2) of it is covered by water. The total area is 11.81% water.

Allegan is located in the Eastern Standard Time (EST) timezone, GMT-05:00. It observes Daylight Saving Time (DST).